| 研究生: |
顏志傑 Yen, Chih-Chieh |
|---|---|
| 論文名稱: |
探討消化道癌症中腫瘤源生標靶與調控免疫微環境之連結 Elucidating the Links of Tumor-derived Targets and Immune Microenvironmental Modulations in Digestive Tract Cancers |
| 指導教授: |
沈延盛
Shan, Yan-Shen 顏家瑞 Yen, Chia-Jui |
| 學位類別: |
博士 Doctor |
| 系所名稱: |
醫學院 - 臨床醫學研究所 Institute of Clinical Medicine |
| 論文出版年: | 2025 |
| 畢業學年度: | 113 |
| 語文別: | 英文 |
| 論文頁數: | 117 |
| 中文關鍵詞: | 消化道癌 、免疫 、標靶 、腫瘤微環境 |
| 外文關鍵詞: | digestive tract cancer, immune, target, tumor microenvironment |
| 相關次數: | 點閱:71 下載:0 |
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消化道由其內生之屏障生理功能與刺激物、致癌物與微生物相產生複雜的癌細胞免疫平衡。免疫檢查點抑制療法 (ICPi) 能增強免疫誘發癌細胞死亡。然而,大多數消化道癌患者均未能成功誘導出滿意的治療效應,因此了解腫瘤源生標靶與免疫治療顯得相當重要。本論文之目的旨為探索與驗證消化道癌中抗癌免疫監測作用下腫瘤源生標靶與免疫微環境的關係與生物機制。首先,本文中觀察到膽管癌腫瘤表面之Globo H與PD-L1之關聯並與抑制性腫瘤浸潤免疫細胞 (Timc) 之豐富度相關。再者,帶有N6-腺苷酸甲基化調控之胃癌透過增強PD-L1表現促進免疫脫逃作用,特別是HER2過表現之胃癌。再者,我們發現合併肝細胞膽管癌中Timc和B型肝炎感染與較佳預後有關,而較豐富的Timc與B型肝炎病毒感染之腫瘤較似於肝細胞癌而非膽管癌。最後,我們發現帶有驅動基因變異例如RET之多種消化道腫瘤針對ICPi療法有較差的療效。總結來說,腫瘤源生標靶能改變消化道腫瘤之免疫微環境,本文所發現能提供決定抗癌免疫療法的路徑並可能將免疫抗性高之”冷腫瘤”轉變為活性高之”熱腫瘤”,結果或可提供困難治療之消化道癌症一項較佳的治療策略。
Digestive tract is known for its inherent physiological function as a barrier to stimulants, carcinogens or microbiomes and involves delicate interplay of cancer immune equilibrium. Immune checkpoint inhibitor (ICPi) therapies enhance the immunogenic cell death. However, it fails to generate a satisfactory response for most patients and highlights the research demand for elucidating tumor-derived targets in immunotherapy. The aim of the dissertation was to explore and validate tumor-derived targets and their correlations with immune microenvironment and biological properties concerning antitumor immune surveillance in digestive tract cancers. In the dissertation, we first observed tumor Globo H and its association with surface programmed death ligand-1 (PD-L1) and enrichment of suppressive tumor infiltrating immune cells (Timcs) in cholangiocarcinoma. Secondly, we observed that m6A regulation potentiated immune evasive condition via up-regulating PD-L1 expression predominantly in HER2-enriched gastric cancer. In addition, we discovered that Timcs and hepatitis B virus (HBV) infection were relevant prognostic factors in combined hepatocellular cholangiocarcinoma (cHCC-CCA). Timcs-enriched and HBV-infected tumors resembled primary HCC but not CCA. Finally, we disclosed that genomic driver alterations, such as RET, correlated with a blunted response to ICPi therapy across several digestive tract cancers. In conclusion, tumor-derived targets affect the immune microenvironment in digestive tract cancers. The information provides access to decipher antitumor immunotherapy and transform the immune evasive “cold” tumors into the reactive “hot” ones. It may optimize the therapeutic benefits in difficult-to-treat digestive tract cancers.
1. Danpanichkul P, Suparan K, Tothanarungroj P, et al. Epidemiology of gastrointestinal cancers: a systematic analysis from the Global Burden of Disease Study 2021. Gut. 2024:gutjnl-2024-333227.
2. Chong X, Madeti Y, Cai J, et al. Recent developments in immunotherapy for gastrointestinal tract cancers. Journal of Hematology & Oncology. 2024;17(1):65.
3. O'Reilly EM, Ko AH. Precision Medicine and Immunotherapy in GI Cancers. Journal of Clinical Oncology. 2022;40(24):2659-2661.
4. Noori M, Jafari-Raddani F, Davoodi-Moghaddam Z, Delshad M, Safiri S, Bashash D. Immune checkpoint inhibitors in gastrointestinal malignancies: an Umbrella review. Cancer Cell International. 2024;24(1):10.
5. Angerilli V, Rojas JJA, Fassan M. Chapter 4 - Immunotherapy in gastrointestinal cancers: Spotlight on the pivotal role of currently available biomarkers. In: Ghidini M, ed. Principles of Immunotherapy Breast and Gastrointestinal Cancers. Academic Press; 2025:83-102.
6. Wattanavises S, Silsirivanit A, Sawanyawisuth K, et al. Increase of MAL-II Binding Alpha2,3-Sialylated Glycan Is Associated with 5-FU Resistance and Short Survival of Cholangiocarcinoma Patients. Medicina (Kaunas, Lithuania). 2019;55(12).
7. Indramanee S, Sawanyawisuth K, Silsirivanit A, et al. Terminal fucose mediates progression of human cholangiocarcinoma through EGF/EGFR activation and the Akt/Erk signaling pathway. Scientific reports. 2019;9(1):17266.
8. Silsirivanit A. Glycans: potential therapeutic targets for cholangiocarcinoma and their therapeutic and diagnostic implications. Expert Opinion on Therapeutic Targets. 2021;25(1):1-4.
9. Pinho SS, Reis CA. Glycosylation in cancer: mechanisms and clinical implications. Nat Rev Cancer. 2015;15(9):540-555.
10. Cagnoni AJ, Pérez Sáez JM, Rabinovich GA, Mariño KV. Turning-Off Signaling by Siglecs, Selectins, and Galectins: Chemical Inhibition of Glycan-Dependent Interactions in Cancer. Frontiers in oncology. 2016;6:109.
11. Hakomori SI. Structure and function of glycosphingolipids and sphingolipids: recollections and future trends. Biochimica et biophysica acta. 2008;1780(3):325-346.
12. S Sigal D, J Hermel D, Hsu P, Pearce T. The role of Globo H and SSEA-4 in the development and progression of cancer, and their potential as therapeutic targets. Future Oncology. 2022;18(1):117-134.
13. Pearce OMT. Cancer glycan epitopes: biosynthesis, structure and function. Glycobiology. 2018;28(9):670-696.
14. Lou Y-W, Wang P-Y, Yeh S-C, et al. Stage-specific embryonic antigen-4 as a potential therapeutic target in glioblastoma multiforme and other cancers. Proceedings of the National Academy of Sciences. 2014;111(7):2482-2487.
15. Zhang S, Cordon-Cardo C, Zhang HS, et al. Selection of tumor antigens as targets for immune attack using immunohistochemistry: I. Focus on gangliosides. International journal of cancer. 1997;73(1):42-49.
16. Martignone S, Menard S, Bedini A, et al. Study of the expression and function of the tumour-associated antigen CaMBr1 in small cell lung carcinomas. Eur J Cancer. 1993;29A(14):2020-2025.
17. Chen I-J, Yang M-C, Chen Y-J. Abstract 2946: The prevalence of Globo H in different tumor types: Breast, pancreatic, lung, gastric, colorectal, liver, and esophageal cancers. Cancer Research. 2020;80(16_Supplement):2946-2946.
18. Liu Y-Y, Gupta V, Patwardhan GA, et al. Glucosylceramide synthase upregulates MDR1 expression in the regulation of cancer drug resistance through cSrc and β-catenin signaling. Molecular Cancer. 2010;9(1):145.
19. Chuang PK, Hsiao M, Hsu TL, et al. Signaling pathway of globo-series glycosphingolipids and β1,3-galactosyltransferase V (β3GalT5) in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(9):3518-3523.
20. Tsai Y-C, Huang J-R, Cheng J-Y, et al. A Prevalent Cancer Associated Glycan, Globo H Ceramide, Induces Immunosuppression by Reducing Notch1 Signaling. Journal of Cancer Science & Therapy. 2013;5:264-270.
21. Fontugne J, Augustin J, Pujals A, et al. PD-L1 expression in perihilar and intrahepatic cholangiocarcinoma. Oncotarget. 2017;8(15):24644-24651.
22. Mavros MN, Economopoulos KP, Alexiou VG, Pawlik TM. Treatment and Prognosis for Patients With Intrahepatic Cholangiocarcinoma: Systematic Review and Meta-analysis. JAMA Surgery. 2014;149(6):565-574.
23. Mirallas O, López-Valbuena D, García-Illescas D, et al. Advances in the systemic treatment of therapeutic approaches in biliary tract cancer. ESMO Open. 2022;7(3).
24. Moris D, Palta M, Kim C, Allen PJ, Morse MA, Lidsky ME. Advances in the treatment of intrahepatic cholangiocarcinoma: An overview of the current and future therapeutic landscape for clinicians. CA: A Cancer Journal for Clinicians. 2023;73(2):198-222.
25. Cheng C-Y, Chen C-P, Wu C-E. Precision Medicine in Cholangiocarcinoma: Past, Present, and Future. Life. 2022;12(6):829.
26. Oh D-Y, He AR, Qin S, et al. Durvalumab plus Gemcitabine and Cisplatin in Advanced Biliary Tract Cancer. NEJM Evidence. 2022;1(8):EVIDoa2200015.
27. Kelley RK, Ueno M, Yoo C, et al. Pembrolizumab in combination with gemcitabine and cisplatin compared with gemcitabine and cisplatin alone for patients with advanced biliary tract cancer (KEYNOTE-966): a randomised, double-blind, placebo-controlled, phase 3 trial. The Lancet.
28. Bang YJ, Van Cutsem E, Feyereislova A, et al. Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial. Lancet (London, England). 2010;376(9742):687-697.
29. Wilke H, Muro K, Van Cutsem E, et al. Ramucirumab plus paclitaxel versus placebo plus paclitaxel in patients with previously treated advanced gastric or gastro-oesophageal junction adenocarcinoma (RAINBOW): a double-blind, randomised phase 3 trial. The Lancet Oncology. 2014;15(11):1224-1235.
30. Shitara K, Lordick F, Bang Y-J, et al. Zolbetuximab plus mFOLFOX6 in patients with CLDN18.2-positive, HER2-negative, untreated, locally advanced unresectable or metastatic gastric or gastro-oesophageal junction adenocarcinoma (SPOTLIGHT): a multicentre, randomised, double-blind, phase 3 trial. The Lancet. 2023;401(10389):1655-1668.
31. Gordon A, Johnston E, Lau DK, Starling N. Targeting FGFR2 Positive Gastroesophageal Cancer: Current and Clinical Developments. OncoTargets and therapy. 2022;15:1183-1196.
32. Akiyama T, Sudo C, Ogawara H, Toyoshima K, Yamamoto T. The product of the human c-erbB-2 gene: a 185-kilodalton glycoprotein with tyrosine kinase activity. Science. 1986;232(4758):1644-1646.
33. Ma C, Wang X, Guo J, Yang B, Li Y. Challenges and future of HER2-positive gastric cancer therapy. Frontiers in oncology. 2023;13:1080990.
34. Van Cutsem E, Bang YJ, Feng-Yi F, et al. HER2 screening data from ToGA: targeting HER2 in gastric and gastroesophageal junction cancer. Gastric Cancer. 2015;18(3):476-484.
35. Abrahao-Machado LF, Scapulatempo-Neto C. HER2 testing in gastric cancer: An update. World J Gastroenterol. 2016;22(19):4619-4625.
36. Grillo F, Fassan M, Sarocchi F, Fiocca R, Mastracci L. HER2 heterogeneity in gastric/gastroesophageal cancers: From benchside to practice. World J Gastroenterol. 2016;22(26):5879-5887.
37. Pathmanathan N, Geng JS, Li W, et al. Human epidermal growth factor receptor 2 status of gastric cancer patients in Asia: results from a large, multicountry study. Asia Pac J Clin Oncol. 2017;13(3):249-260.
38. Kim WH, Gomez-Izquierdo L, Vilardell F, et al. HER2 Status in Gastric and Gastroesophageal Junction Cancer: Results of the Large, Multinational HER-EAGLE Study. Appl Immunohistochem Mol Morphol. 2018;26(4):239-245.
39. Cen S, Xu H, Liu Z, Zhao R, Pan H, Han W. Immune microenvironment characteristics and their implications for immune checkpoint inhibitor efficacy in HER2-overexpressing gastric cancer. Clinical and Experimental Immunology. 2022;207(3):318-328.
40. Kwon HJ, Park Y, Nam SK, et al. Genetic and immune microenvironment characterization of HER2-positive gastric cancer: Their association with response to trastuzumab-based treatment. Cancer Medicine. 2023;12(9):10371-10384.
41. Janjigian YY, Kawazoe A, Yañez P, et al. The KEYNOTE-811 trial of dual PD-1 and HER2 blockade in HER2-positive gastric cancer. Nature. 2021;600(7890):727-730.
42. He C. Grand Challenge Commentary: RNA epigenetics? Nature Chemical Biology. 2010;6(12):863-865.
43. Barbieri I, Kouzarides T. Role of RNA modifications in cancer. Nature Reviews Cancer. 2020;20(6):303-322.
44. Huang H, Weng H, Sun W, et al. Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nature Cell Biology. 2018;20(3):285-295.
45. Sun CY, Cao D, Du BB, Chen CW, Liu D. The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m(6)A readers in cancer. International journal of biological sciences. 2022;18(7):2744-2758.
46. Huang W, Chen T-Q, Fang K, Zeng Z-C, Ye H, Chen Y-Q. N6-methyladenosine methyltransferases: functions, regulation, and clinical potential. Journal of Hematology & Oncology. 2021;14(1):117.
47. Bai Y, Li K, Peng J, Yi C. m6A modification: a new avenue for anti-cancer therapy. Life Medicine. 2023;2(1).
48. Yang D-D, Chen Z-H, Yu K, et al. METTL3 Promotes the Progression of Gastric Cancer via Targeting the MYC Pathway. Frontiers in oncology. 2020;10.
49. Qin Q, Fang DL, Zhou W, Meng Y, Wei J. Classification and immune invasion analysis of breast cancer based on m6A genes. Annals of translational medicine. 2021;9(18):1418.
50. Cao X, Geng Q, Fan D, et al. m6A methylation: a process reshaping the tumour immune microenvironment and regulating immune evasion. Molecular Cancer. 2023;22(1):42.
51. Wan W, Ao X, Chen Q, et al. METTL3/IGF2BP3 axis inhibits tumor immune surveillance by upregulating N(6)-methyladenosine modification of PD-L1 mRNA in breast cancer. Mol Cancer. 2022;21(1):60.
52. Zhang W, Xiao P, Tang J, et al. m6A Regulator-Mediated Tumour Infiltration and Methylation Modification in Cervical Cancer Microenvironment. Frontiers in Immunology. 2022;13.
53. Chen S, Su X, Wang J, et al. Identification and Validation of METTL3-Related Molecules for Predicting Prognosis and Efficacy of Immunotherapy in Gastric Cancer Based on m6A Methylome and Transcriptome Sequencing Analysis. Frontiers in oncology. 2022;12.
54. Shriwas O, Mohapatra P, Mohanty S, Dash R. The Impact of m6A RNA Modification in Therapy Resistance of Cancer: Implication in Chemotherapy, Radiotherapy, and Immunotherapy. Frontiers in oncology. 2020;10:612337.
55. N H, AM N, M K, et al. SEER Cancer Statistics Review, 1975-2018. National Cancer Institute. 2020.
56. Morgan E, Arnold M, Camargo MC, et al. The current and future incidence and mortality of gastric cancer in 185 countries, 2020–40: A population-based modelling study. eClinicalMedicine. 2022;47.
57. Wagner AD, Unverzagt S, Grothe W, et al. Chemotherapy for advanced gastric cancer. The Cochrane database of systematic reviews. 2010(3):Cd004064.
58. Schwartz GK. Invasion and metastases in gastric cancer: in vitro and in vivo models with clinical correlations. Seminars in oncology. 1996;23(3):316-324.
59. Zavros Y, Merchant JL. The immune microenvironment in gastric adenocarcinoma. Nature Reviews Gastroenterology & Hepatology. 2022;19(7):451-467.
60. Kang YK, Boku N, Satoh T, et al. Nivolumab in patients with advanced gastric or gastro-oesophageal junction cancer refractory to, or intolerant of, at least two previous chemotherapy regimens (ONO-4538-12, ATTRACTION-2): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet (London, England). 2017;390(10111):2461-2471.
61. Janjigian YY, Shitara K, Moehler M, et al. First-line nivolumab plus chemotherapy versus chemotherapy alone for advanced gastric, gastro-oesophageal junction, and oesophageal adenocarcinoma (CheckMate 649): a randomised, open-label, phase 3 trial. Lancet (London, England). 2021;398(10294):27-40.
62. Sahin U, Türeci Ö, Manikhas G, et al. FAST: a randomised phase II study of zolbetuximab (IMAB362) plus EOX versus EOX alone for first-line treatment of advanced CLDN18.2-positive gastric and gastro-oesophageal adenocarcinoma. Annals of Oncology. 2021;32(5):609-619.
63. Budhu A, Pehrsson EC, He A, et al. Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy. Cell Reports Medicine. 2023;4(6):101052.
64. Canale FP, Neumann J, von Renesse J, et al. Proteomics of immune cells from liver tumors reveals immunotherapy targets. Cell Genomics. 2023;3(6):100331.
65. Lim CJ, Lee YH, Pan L, et al. Multidimensional analyses reveal distinct immune microenvironment in hepatitis B virus-related hepatocellular carcinoma. Gut. 2019;68(5):916.
66. Li B, Yan C, Zhu J, et al. Anti–PD-1/PD-L1 Blockade Immunotherapy Employed in Treating Hepatitis B Virus Infection–Related Advanced Hepatocellular Carcinoma: A Literature Review. Frontiers in Immunology. 2020;11.
67. Yoon YI, Hwang S, Lee YJ, et al. Postresection Outcomes of Combined Hepatocellular Carcinoma-Cholangiocarcinoma, Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma. Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract. 2016;20(2):411-420.
68. Portolani N, Baiocchi GL, Coniglio A, et al. Intrahepatic cholangiocarcinoma and combined hepatocellular-cholangiocarcinoma: a Western experience. Annals of surgical oncology. 2008;15(7):1880-1890.
69. Gera S, Ettel M, Acosta-Gonzalez G, Xu R. Clinical features, histology, and histogenesis of combined hepatocellular-cholangiocarcinoma. World journal of hepatology. 2017;9(6):300-309.
70. Stavraka C, Rush H, Ross P. Combined hepatocellular cholangiocarcinoma (cHCC-CC): an update of genetics, molecular biology, and therapeutic interventions. J Hepatocell Carcinoma. 2018;6:11-21.
71. Govaere O, Wouters J, Petz M, et al. Laminin-332 sustains chemoresistance and quiescence as part of the human hepatic cancer stem cell niche. J Hepatol. 2016;64(3):609-617.
72. Moeini A, Sia D, Zhang Z, et al. Mixed hepatocellular cholangiocarcinoma tumors: Cholangiolocellular carcinoma is a distinct molecular entity. J Hepatol. 2017;66(5):952-961.
73. Maximin S, Ganeshan DM, Shanbhogue AK, et al. Current update on combined hepatocellular-cholangiocarcinoma. European journal of radiology open. 2014;1:40-48.
74. Satoh T, Xu R-H, Chung HC, et al. Lapatinib Plus Paclitaxel Versus Paclitaxel Alone in the Second-Line Treatment of HER2-Amplified Advanced Gastric Cancer in Asian Populations: TyTAN—A Randomized, Phase III Study. Journal of Clinical Oncology. 2014;32(19):2039-2049.
75. Fujii H, Zhu XG, Matsumoto T, et al. Genetic classification of combined hepatocellular-cholangiocarcinoma. Hum Pathol. 2000;31(9):1011-1017.
76. Zuo HQ, Yan LN, Zeng Y, et al. Clinicopathological characteristics of 15 patients with combined hepatocellular carcinoma and cholangiocarcinoma. Hepatobiliary & pancreatic diseases international : HBPD INT. 2007;6(2):161-165.
77. Lee JH, Chung GE, Yu SJ, et al. Long-term prognosis of combined hepatocellular and cholangiocarcinoma after curative resection comparison with hepatocellular carcinoma and cholangiocarcinoma. Journal of clinical gastroenterology. 2011;45(1):69-75.
78. Okuda K. Natural history of hepatocellular carcinoma including fibrolamellar and hepato-cholangiocarcinoma variants. Journal of gastroenterology and hepatology. 2002;17(4):401-405.
79. Yeh MM. Pathology of combined hepatocellular-cholangiocarcinoma. Journal of gastroenterology and hepatology. 2010;25(9):1485-1492.
80. Theise ND, Yao JL, Harada K, et al. Hepatic 'stem cell' malignancies in adults: four cases. Histopathology. 2003;43(3):263-271.
81. Allen RA, Lisa JR. Combined liver cell and bile duct carcinoma. The American journal of pathology. 1949;25(4):647-655.
82. Goodman ZD, Ishak KG, Langloss JM, Sesterhenn IA, Rabin L. Combined hepatocellular-cholangiocarcinoma. A histologic and immunohistochemical study. Cancer. 1985;55(1):124-135.
83. Nagtegaal ID, Odze RD, Klimstra D, et al. The 2019 WHO classification of tumours of the digestive system. Histopathology. 2020;76(2):182-188.
84. Brunt E, Aishima S, Clavien PA, et al. cHCC-CCA: Consensus terminology for primary liver carcinomas with both hepatocytic and cholangiocytic differentation. Hepatology. 2018.
85. Flejou JF. [WHO Classification of digestive tumors: the fourth edition]. Annales de pathologie. 2011;31(5 Suppl):S27-31.
86. Kim H, Park YN. Hepatocellular carcinomas expressing 'stemness'-related markers: clinicopathological characteristics. Dig Dis. 2014;32(6):778-785.
87. Chan AWH, Tong JHM, Chan SL, Lai PBS, To K-F. Expression of stemness markers (CD133 and EpCAM) in prognostication of hepatocellular carcinoma. Histopathology. 2014;64(7):935-950.
88. Brunt EM, Paradis V, Sempoux C, Theise ND. Biphenotypic (hepatobiliary) primary liver carcinomas: the work in progress. Hepat Oncol. 2015;2(3):255-273.
89. Pinter M, Scheiner B, Pinato DJ. Immune checkpoint inhibitors in hepatocellular carcinoma: emerging challenges in clinical practice. The Lancet Gastroenterology & Hepatology. 2023;8(8):760-770.
90. Calles A, Riess JW, Brahmer JR. Checkpoint Blockade in Lung Cancer With Driver Mutation: Choose the Road Wisely. American Society of Clinical Oncology Educational Book. 2020(40):372-384.
91. Yan D. Hope and Challenges: Immunotherapy in EGFR-Mutant NSCLC Patients. Biomedicines. 2023;11(11):2916.
92. Belli C, Anand S, Gainor JF, et al. Progresses Toward Precision Medicine in RET-altered Solid Tumors. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020;26(23):6102-6111.
93. Verrienti A, Grani G, Sponziello M, et al. Precision oncology for RET-related tumors. Frontiers in oncology. 2022;12:992636-992636.
94. Mulligan LM. RET revisited: expanding the oncogenic portfolio. Nat Rev Cancer. 2014;14(3):173-186.
95. Mulligan LM, Kwok JB, Healey CS, et al. Germ-line mutations of the RET proto-oncogene in multiple endocrine neoplasia type 2A. Nature. 1993;363(6428):458-460.
96. Hofstra RM, Landsvater RM, Ceccherini I, et al. A mutation in the RET proto-oncogene associated with multiple endocrine neoplasia type 2B and sporadic medullary thyroid carcinoma. Nature. 1994;367(6461):375-376.
97. Takeuchi K, Soda M, Togashi Y, et al. RET, ROS1 and ALK fusions in lung cancer. Nature medicine. 2012;18(3):378-381.
98. Wirth LJ, Sherman E, Robinson B, et al. Efficacy of Selpercatinib in RET-Altered Thyroid Cancers. New England Journal of Medicine. 2020;383(9):825-835.
99. Drilon A, Oxnard GR, Tan DSW, et al. Efficacy of Selpercatinib in RET Fusion–Positive Non–Small-Cell Lung Cancer. New England Journal of Medicine. 2020;383(9):813-824.
100. Gainor JF, Curigliano G, Kim D-W, et al. Pralsetinib for RET fusion-positive non-small-cell lung cancer (ARROW): a multi-cohort, open-label, phase 1/2 study. The Lancet Oncology. 2021;22(7):959-969.
101. Subbiah V, Hu MI, Wirth LJ, et al. Pralsetinib for patients with advanced or metastatic RET-altered thyroid cancer (ARROW): a multi-cohort, open-label, registrational, phase 1/2 study. The Lancet Diabetes & Endocrinology. 2021;9(8):491-501.
102. Wang R, Hu H, Pan Y, et al. RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2012;30(35):4352-4359.
103. Hackshaw A, Fajardo O, Dafni U, et al. Characteristics and Survival Outcomes of Patients With Metastatic <i>RET</i> Fusion–Positive Solid Tumors Receiving Non-RET Inhibitor Standards of Care in a Real-World Setting. JCO Precis Oncol. 2024(8):e2300334.
104. AACR Project GENIE: Powering Precision Medicine through an International Consortium. Cancer discovery. 2017;7(8):818-831.
105. Adashek JJ, Desai AP, Andreev-Drakhlin AY, Roszik J, Cote GJ, Subbiah V. Hallmarks of RET and Co-occuring Genomic Alterations in RET-aberrant Cancers. Molecular Cancer Therapeutics. 2021;20(10):1769-1776.
106. Kato S, Subbiah V, Marchlik E, Elkin SK, Carter JL, Kurzrock R. RET Aberrations in Diverse Cancers: Next-Generation Sequencing of 4,871 Patients. Clinical cancer research : an official journal of the American Association for Cancer Research. 2017;23(8):1988-1997.
107. Zhao Z, Fu T, Gao J, et al. Identifying novel oncogenic <em>RET</em> mutations and characterising their sensitivity to RET-specific inhibitors. Journal of Medical Genetics. 2021;58(2):79.
108. Hegde A, Andreev-Drakhlin AY, Roszik J, et al. Responsiveness to immune checkpoint inhibitors versus other systemic therapies in RET-aberrant malignancies. ESMO Open. 2020;5(5):e000799.
109. Offin M, Guo R, Wu SL, et al. Immunophenotype and Response to Immunotherapy of RET-Rearranged Lung Cancers. JCO Precis Oncol. 2019;3:PO.18.00386.
110. Kuo T-M, Luo S-Y, Chiang S-L, et al. Arecoline induces TNF-alpha production and Zonula Occludens-1 redistribution in mouse Sertoli TM4 cells. Journal of Biomedical Science. 2014;21(1):93.
111. Klintrup K, Mäkinen JM, Kauppila S, et al. Inflammation and prognosis in colorectal cancer. Eur J Cancer. 2005;41(17):2645-2654.
112. Xiao Y, Lin M, Jiang X, et al. The Recent Advances on Liver Cancer Stem Cells: Biomarkers, Separation, and Therapy. Analytical Cellular Pathology. 2017;2017:5108653.
113. Ishak K, Baptista A, Bianchi L, et al. Histological grading and staging of chronic hepatitis. J Hepatol. 1995;22(6):696-699.
114. Landrum MJ, Chitipiralla S, Brown GR, et al. ClinVar: improvements to accessing data. Nucleic acids research. 2020;48(D1):D835-d844.
115. Cerami E, Gao J, Dogrusoz U, et al. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer discovery. 2012;2(5):401-404.
116. Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science signaling. 2013;6(269):pl1.
117. Sondka Z, Bamford S, Cole CG, Ward SA, Dunham I, Forbes SA. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat Rev Cancer. 2018;18(11):696-705.
118. Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human genetics. 2014;133(1):1-9.
119. Väyrynen JP, Tuomisto A, Klintrup K, Mäkelä J, Karttunen TJ, Mäkinen MJ. Detailed analysis of inflammatory cell infiltration in colorectal cancer. British Journal of Cancer. 2013;109(7):1839-1847.
120. Schwartz LH, Litière S, de Vries E, et al. RECIST 1.1-Update and clarification: From the RECIST committee. European journal of cancer (Oxford, England : 1990). 2016;62:132-137.
121. Chang K, Creighton CJ, Davis C, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics. 2013;45(10):1113-1120.
122. Lonsdale J, Thomas J, Salvatore M, et al. The Genotype-Tissue Expression (GTEx) project. Nature Genetics. 2013;45(6):580-585.
123. Chaisaingmongkol J, Budhu A, Dang H, et al. Common Molecular Subtypes Among Asian Hepatocellular Carcinoma and Cholangiocarcinoma. Cancer cell. 2017;32(1):57-70.e53.
124. Győrffy B. Integrated analysis of public datasets for the discovery and validation of survival-associated genes in solid tumors. Innovation (Cambridge (Mass)). 2024;5(3):100625.
125. Li T, Fu J, Zeng Z, et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic acids research. 2020;48(W1):W509-w514.
126. Ma L, Heinrich S, Wang L, et al. Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancer. Nature communications. 2022;13(1):7533.
127. Hao Y, Stuart T, Kowalski MH, et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nature Biotechnology. 2024;42(2):293-304.
128. Hao Y, Hao S, Andersen-Nissen E, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184(13):3573-3587.e3529.
129. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences. 2005;102(43):15545-15550.
130. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological). 1995;57(1):289-300.
131. Posta M, Győrffy B. Analysis of a large cohort of pancreatic cancer transcriptomic profiles to reveal the strongest prognostic factors. Clinical and Translational Science. 2023;16(8):1479-1491.
132. Kovács SA, Fekete JT, Győrffy B. Predictive biomarkers of immunotherapy response with pharmacological applications in solid tumors. Acta Pharmacologica Sinica. 2023;44(9):1879-1889.
133. Li T, Fan J, Wang B, et al. TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells. Cancer Res. 2017;77(21):e108-e110.
134. Li B, Severson E, Pignon JC, et al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome biology. 2016;17(1):174.
135. Banales JM, Marin JJG, Lamarca A, et al. Cholangiocarcinoma 2020: the next horizon in mechanisms and management. Nature Reviews Gastroenterology & Hepatology. 2020;17(9):557-588.
136. Hung TH, Hung JT, Wu CE, et al. Globo H Is a Promising Theranostic Marker for Intrahepatic Cholangiocarcinoma. Hepatology communications. 2022;6(1):194-208.
137. Kuo H-H, Lin R-J, Hung J-T, et al. High expression FUT1 and B3GALT5 is an independent predictor of postoperative recurrence and survival in hepatocellular carcinoma. Scientific reports. 2017;7(1):10750.
138. Liao Y-M, Wang Y-H, Hung J-T, et al. High B3GALT5 expression confers poor clinical outcome and contributes to tumor progression and metastasis in breast cancer. Breast Cancer Research. 2021;23(1):5.
139. Hung TH, Yeh CN, Hung JT, et al. Globo H ceramide is an independent prognostic marker for gallbladder cancer. American journal of cancer research. 2023;13(10):4811-4821.
140. Kawai S, Kato S, Imai H, Okada Y, Ishioka C. Suppression of FUT1 attenuates cell proliferation in the HER2-overexpressing cancer cell line NCI-N87. Oncology reports. 2013;29(1):13-20.
141. Lai T-Y, Chen IJ, Lin R-J, et al. Fucosyltransferase 1 and 2 play pivotal roles in breast cancer cells. Cell Death Discovery. 2019;5(1):74.
142. Chang WW, Lee CH, Lee P, et al. Expression of Globo H and SSEA3 in breast cancer stem cells and the involvement of fucosyl transferases 1 and 2 in Globo H synthesis. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(33):11667-11672.
143. Wang SH, Cheng JY, Tsai HH, et al. Conformational alteration in glycan induces phospholipase Cbeta1 activation and angiogenesis. J Biomed Sci. 2022;29(1):105.
144. Cheng JY, Wang SH, Lin J, et al. Globo-H ceramide shed from cancer cells triggers translin-associated factor X-dependent angiogenesis. Cancer Res. 2014;74(23):6856-6866.
145. Liu Z, Ning F, Cai Y, et al. The EGFR-P38 MAPK axis up-regulates PD-L1 through miR-675-5p and down-regulates HLA-ABC via hexokinase-2 in hepatocellular carcinoma cells. Cancer Communications. 2021;41(1):62-78.
146. Chen N, Fang W, Zhan J, et al. Upregulation of PD-L1 by EGFR Activation Mediates the Immune Escape in EGFR-Driven NSCLC: Implication for Optional Immune Targeted Therapy for NSCLC Patients with EGFR Mutation. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer. 2015;10(6):910-923.
147. Cha JH, Chan LC, Li CW, Hsu JL, Hung MC. Mechanisms Controlling PD-L1 Expression in Cancer. Molecular cell. 2019;76(3):359-370.
148. Peng S, Wang R, Zhang X, et al. EGFR-TKI resistance promotes immune escape in lung cancer via increased PD-L1 expression. Molecular Cancer. 2019;18(1):165.
149. Chen HN, Liang KH, Lai JK, et al. EpCAM Signaling Promotes Tumor Progression and Protein Stability of PD-L1 through the EGFR Pathway. Cancer Res. 2020;80(22):5035-5050.
150. Job S, Rapoud D, Dos Santos A, et al. Identification of Four Immune Subtypes Characterized by Distinct Composition and Functions of Tumor Microenvironment in Intrahepatic Cholangiocarcinoma. Hepatology. 2020;72(3):965-981.
151. Martin-Serrano MA, Kepecs B, Torres-Martin M, et al. Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications. Gut. 2023;72(4):736-748.
152. Tomlinson JL, Valle JW, Ilyas SI. Immunobiology of cholangiocarcinoma. Journal of Hepatology. 2023;79(3):867-875.
153. Tsimberidou AM, Ajani JA, Hsu P, Chen I-J, Pearce TE. A phase I/II, open-label, dose-escalation, and cohort-expansion study evaluating the safety, pharmacokinetics, and therapeutic activity of OBI-999 in patients with advanced solid tumors. Journal of Clinical Oncology. 2020;38(15_suppl):TPS3657-TPS3657.
154. Huang CS, Yu AL, Tseng LM, et al. Globo H-KLH vaccine adagloxad simolenin (OBI-822)/OBI-821 in patients with metastatic breast cancer: phase II randomized, placebo-controlled study. Journal for immunotherapy of cancer. 2020;8(2).
155. Hung JT, Chen IJ, Ueng SH, et al. The clinical relevance of humoral immune responses to Globo H-KLH vaccine adagloxad simolenin (OBI-822)/OBI-821 and expression of Globo H in metastatic breast cancer. Journal for immunotherapy of cancer. 2022;10(6).
156. Scott GK, Marx C, Berger CE, et al. Destabilization of ERBB2 transcripts by targeting 3' untranslated region messenger RNA associated HuR and histone deacetylase-6. Molecular cancer research : MCR. 2008;6(7):1250-1258.
157. Sun C, Wang A, Zhou Y, et al. Spatially resolved multi-omics highlights cell-specific metabolic remodeling and interactions in gastric cancer. Nature communications. 2023;14(1):2692.
158. Hu Y, Zhao L, Li Z, Dong X, Xu T, Zhao Y. Classifying the multi-omics data of gastric cancer using a deep feature selection method. Expert Systems with Applications. 2022;200:116813.
159. Bass AJ, Thorsson V, Shmulevich I, et al. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513(7517):202-209.
160. Cristescu R, Lee J, Nebozhyn M, et al. Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes. Nature medicine. 2015;21(5):449-456.
161. Lee CH, Hsieh SY, Chang CJ, Lin YJ. Comparison of clinical characteristics of combined hepatocellular-cholangiocarcinoma and other primary liver cancers. Journal of gastroenterology and hepatology. 2013;28(1):122-127.
162. Zhan Q, Shen BY, Deng XX, et al. Clinical and pathological analysis of 27 patients with combined hepatocellular-cholangiocarcinoma in an Asian center. Journal of hepato-biliary-pancreatic sciences. 2012;19(4):361-369.
163. Zuo C, Xia M, Wu Q, Zhu H, Liu J, Liu C. Role of antiviral therapy in reducing recurrence and improving survival in hepatitis B virus-associated hepatocellular carcinoma following curative resection (Review). Oncol Lett. 2015;9(2):527-534.
164. Du Q, Yuan J, Ren Z. Hepatocellular Carcinoma Patients with Hepatitis B Virus Infection Exhibited Favorable Survival from Immune Checkpoint Inhibitors: A Systematic Review and Meta-Analysis. Liver Cancer. 2023;13(4):344-354.
165. Yao W, He J-c, Yang Y, et al. The Prognostic Value of Tumor-infiltrating Lymphocytes in Hepatocellular Carcinoma: a Systematic Review and Meta-analysis. Scientific reports. 2017;7(1):7525.
166. Jeon J, Maeng LS, Bae YJ, Lee EJ, Yoon YC, Yoon N. Comparing Clonality Between Components of Combined Hepatocellular Carcinoma and Cholangiocarcinoma by Targeted Sequencing. Cancer Genomics Proteomics. 2018;15(4):291-298.
167. Sasaki M, Sato Y, Nakanuma Y. Mutational landscape of combined hepatocellular carcinoma and cholangiocarcinoma, and its clinicopathological significance. Histopathology. 2017;70(3):423-434.
168. Zehir A, Benayed R, Shah RH, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nature medicine. 2017;23(6):703-713.
169. Wu L, Yao H, Chen H, et al. Landscape of somatic alterations in large-scale solid tumors from an Asian population. Nature communications. 2022;13(1):4264.
170. Bhandari NR, Hess LM, Han Y, Zhu YE, Sireci AN. Efficacy of immune checkpoint inhibitor therapy in patients with RET fusion-positive non-small-cell lung cancer. Immunotherapy. 2021;13(11):893-904.
171. Lee J, Ku BM, Shim JH, et al. Characteristics and outcomes of RET-rearranged Korean non-small cell lung cancer patients in real-world practice. Japanese journal of clinical oncology. 2020;50(5):594-601.
172. Wu G, Guo L, Gu Y, et al. The genomic characteristics of RET fusion positive tumors in Chinese non-small cell lung cancer (NSCLC) patients. Journal of Cancer Research and Clinical Oncology. 2022.
173. Mazieres J, Drilon A, Lusque A, et al. Immune checkpoint inhibitors for patients with advanced lung cancer and oncogenic driver alterations: results from the IMMUNOTARGET registry. Annals of oncology : official journal of the European Society for Medical Oncology. 2019;30(8):1321-1328.
174. Lin X, Wang L, Xie X, et al. Prognostic Biomarker TP53 Mutations for Immune Checkpoint Blockade Therapy and Its Association With Tumor Microenvironment of Lung Adenocarcinoma. Frontiers in Molecular Biosciences. 2020;7.
175. Sun H, Liu S-Y, Zhou J-Y, et al. Specific TP53 subtype as biomarker for immune checkpoint inhibitors in lung adenocarcinoma. EBioMedicine. 2020;60:102990-102990.
176. Mograbi B, Heeke S, Hofman P. The Importance of STK11/LKB1 Assessment in Non-Small Cell Lung Carcinomas. Diagnostics. 2021;11(2):196.
177. Wang H, Guo J, Shang X, Wang Z. Less immune cell infiltration and worse prognosis after immunotherapy for patients with lung adenocarcinoma who harbored STK11 mutation. International Immunopharmacology. 2020;84:106574.